RetrogeneDB ID: retro_rnor_2954

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:95585907..95586330(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Josd1
• Ensembl ID: ENSRNOG00000014440
• Aliases: Josd1, RGD1305388
• Description: Josephin-1 [Source:UniProtKB/Swiss-Prot;Acc:Q5BJY4]

Sequence

>retro_rnor_2954
AAAAGGCTGTCTCCGAACACTGTGGTGACGCCCCACAAGAGCATGCTGTGAAATGGGAATTATGATGTGAATGTCATCAT
GGCGGCCCTTCAAACAAAAGGCTATGAAGCTGTTTGGTGGGACAAGCGCAGGGACGTGGGTGTTATTGCTCTTGCTAACG
TCATGGGCTTCATCATGAACCTGCCCTCCAGCCTGTGCTGGGGTCCACTCAAGTTGCCTCTCAAAAGGCAGCACCGGATC
TGTGTTCGTGAGGTGGGAGGGGCCTACTACAACCTTGACTCCAAACTCAAGATACCAGAGTGGATTGGAGGCGAGAGTGA
GCTCAGGAAATTTCTAAAATACCATTTGCGAGGTAAAAACTGTGAACTCCTACTGGTGGTACTAGAAGAAGTGGAAGCCC
ATCAGAGCTGGAGGGCCGACGTG

Alignment

ORF - retro_rnor_2954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.77 %
• Parental protein coverage: 70.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRLSPNTVVTPHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDKRRDVGVIALANVMGFIMNLPSSLCWGP
          .RLSPNTVVTPHK.SML.NGNYDVNVIMAALQTKGYEAVWWDKRRDVGVIALANVMGFIMNLPSSLCWGP
Retrocopy KRLSPNTVVTPHK-SML*NGNYDVNVIMAALQTKGYEAVWWDKRRDVGVIALANVMGFIMNLPSSLCWGP

Parental  LKLPLKRQHWICVREVGGAYYNLDSKLKMPEWIGGESELRKFLKYHLRGKNCELLLVVPEEVEAHQSWRA
          LKLPLKRQH.ICVREVGGAYYNLDSKLK.PEWIGGESELRKFLKYHLRGKNCELLLVV.EEVEAHQSWRA
Retrocopy LKLPLKRQHRICVREVGGAYYNLDSKLKIPEWIGGESELRKFLKYHLRGKNCELLLVVLEEVEAHQSWRA

Parental  DV
          DV
Retrocopy DV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	52.48 RPM
SRP017611_kidney	0.00 RPM	26.52 RPM
SRP017611_liver	0.00 RPM	23.40 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2954 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2954 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2954 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010171	1 retrocopy	retro_btau_1508,
Canis familiaris	ENSCAFG00000001379	1 retrocopy	retro_cfam_1500,
Choloepus hoffmanni	ENSCHOG00000001723	2 retrocopies	retro_chof_1576, retro_chof_233,
Equus caballus	ENSECAG00000015546	1 retrocopy	retro_ecab_251,
Felis catus	ENSFCAG00000002821	1 retrocopy	retro_fcat_565,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Microcebus murinus	ENSMICG00000011798	1 retrocopy	retro_mmur_1202,
Myotis lucifugus	ENSMLUG00000003764	1 retrocopy	retro_mluc_1868,
Mus musculus	ENSMUSG00000022426	1 retrocopy	retro_mmus_3014,
Otolemur garnettii	ENSOGAG00000007520	3 retrocopies	retro_ogar_1462, retro_ogar_2911, retro_ogar_3487,
Pteropus vampyrus	ENSPVAG00000010148	1 retrocopy	retro_pvam_181,
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954 , retro_rnor_906,
Rattus norvegicus	ENSRNOG00000019442	1 retrocopy	retro_rnor_550,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193,
Tarsius syrichta	ENSTSYG00000008846	1 retrocopy	retro_tsyr_1076,